Implement suggestions from code review

modules/ampir/main.nf

@@ -11,11 +11,11 @@ process AMPIR {
     tuple val(meta), path(faa)
     val cut_off
     val model
-    val output_name
 
     output:
-    tuple val(meta), path(output_name)  , emit: amps
+    tuple val(meta), path("*.faa"), emit: amps_faa
-    path "versions.yml"                 , emit: versions
+    tuple val(meta), path("*.csv"), emit: amps_csv
+    path "versions.yml"           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,10 +27,11 @@ process AMPIR {
     #!/usr/bin/env Rscript
     library(ampir)
 
-    protein_seqs <- read_faa("${faa}")
+    protein_seqs <- read_faa('${faa}')
-    prediction <- predict_amps(protein_seqs, model = '$model')
+    prediction <- predict_amps(protein_seqs, model = '${model}')
-    prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer($cut_off)), ]
+    prediction <- protein_seqs[which(prediction\$prob_AMP >= as.integer(${cut_off})), ]
-    df_to_faa(protein_seqs, '$output_name')
+    df_to_faa(protein_seqs, "${prefix}.faa")
+    write.table(prediction, file = "${prefix}.csv", row.names = FALSE, quote = FALSE, dec = '.')
 
     version_file_path <- "versions.yml"
     version_ampir <- paste(unlist(packageVersion("ampir")), collapse = ".")

modules/ampir/meta.yml

@@ -8,7 +8,7 @@ tools:
   - "ampir":
       description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale."
       homepage: "https://github.com/Legana/ampir"
-      documentation: "https://github.com/Legana/ampir"
+      documentation: "https://cran.r-project.org/web/packages/ampir/index.html"
       tool_dev_url: "https://github.com/Legana/ampir"
       doi: "10.1093/bioinformatics/btaa653"
       licence: ["GPL v2"]
@@ -42,14 +42,14 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - amps:
+  - amps_faa:
       type: file
-      description: File containing AMP predictions
+      description: File containing AMP predictions in amino acid FASTA format
-      pattern: "prediction.fasta"
-  - output_name:
-      type: value
-      description: File name of the FASTA output file
       pattern: "*.{faa,fasta}"
+  - amps_csv:
+      type: file
+      description: File containing AMP predictions in CSV format
+      pattern: "*.csv"
 
 authors:
   - "@jasmezz"

tests/modules/ampir/main.nf

@@ -14,7 +14,5 @@ workflow test_ampir {
 
     model = "precursor"
 
-    output_name = "prediction.fasta"
+    AMPIR ( fasta, cut_off, model )
-
-    AMPIR ( fasta, cut_off, model, output_name )
 }

tests/modules/ampir/test.yml

@@ -1,9 +1,11 @@
-- name: "ampir"
+- name: ampir test_ampir
-  command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config -c ./tests/modules/ampir/nextflow.config
+  command: nextflow run ./tests/modules/ampir -entry test_ampir -c ./tests/config/nextflow.config  -c ./tests/modules/ampir/nextflow.config
   tags:
-    - "ampir"
+    - ampir
   files:
-    - path: output/ampir/prediction.fasta
+    - path: output/ampir/test.csv
+      md5sum: 063fd8866f6a669457d7a49404fb449f
+    - path: output/ampir/test.faa
       md5sum: e605d38752fd90261c924d51f7007189
     - path: output/ampir/versions.yml
       md5sum: 4a11d25b8a904a7ffb34ae88f6826888